Recent studies examining the role of oligodendrocytes in development, and following disease or trauma, have exposed our limited understanding of oligodendrocyte function and underscore the need to establish new tools which will allow us to uncover the full repertoire of proteins regulated by oligodendrocytes and ascertain their function. Unfortunately, the lack of cDNA libraries derived from myelinating oligodendrocytes has hampered attempts to identify proteins derived from or regulated by these cells. We therefore established a new method to elucidate such proteins by coupling the techniques of X-irradiation, 2-D gel electrophoresis, and mass spectrometry. Specifically, in previous studies, we had demonstrated that oligodendrocytes could be selectively eliminated from one optic nerve of a rat by treating the animal to a unilateral exposure of X-irradiation at the time of birth. We further showed that, with time, the X-irradiated optic nerve became repopulated with a second cohort of oligodendrocytes from postnatal day (P) 14 on. This repopulation of cells into the X-irradiated nerve nearly restores the full complement of oligodendrocytes normally found in the optic nerve by P28. Therefore, utilizing this approach, we experimentally created, within the same animal, one optic nerve devoid of oligodendrocytes and their progenitors (the X-irradiated side) and one optic nerve containing the normal oligodendrocyte population (the untreated side). We now provide data demonstrating that 2-D gel protein profiles of normal and X-irradiated rat optic nerves can be compared to quickly isolate, from an in vivo model system, those proteins expressed by oligodendrocytes as well as those expressed by other cells which are regulated by oligendrocytes. The subsequent identification of these oligodendrocyte-associated proteins is accomplished by mass spectrometry. This experimental model system is especially powerful and unique since it retains all of the cell-cell interactions crucial to myelination. Taken together, these experiments should lead to a clearer understanding of the role of oligodendrocytes in CNS development and of the array of proteins associated with myelination.